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Commit message:
planemo upload commit 936a627c4fc706080f07ec678f89e8256a7e7895 |
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modified:
Dockerfile job_conf.yml misc/bioconda-recipes-seqsero2s-meta.yml patch_stringmlst.sh seqsero2S.xml tool-data/all_fasta.loc.sample |
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SeqSero2S/LICENSE SeqSero2S/MANIFEST.in SeqSero2S/README.md SeqSero2S/bin/Initial_Conditions_SS2.py SeqSero2S/bin/Initial_Conditions_SS2S.py SeqSero2S/bin/SeqSero2S.py SeqSero2S/bin/SeqSero2_update_kmer_database.py SeqSero2S/bin/deinterleave_fastq.sh SeqSero2S/seqsero2s_db/H_and_O_and_specific_genes.fasta SeqSero2S/seqsero2s_db/antigens.pickle SeqSero2S/seqsero2s_db/invA_mers_dict SeqSero2S/seqsero2s_db/kmer/salmonella.log SeqSero2S/seqsero2s_db/kmer/salmonella_35.txt SeqSero2S/seqsero2s_db/kmer/salmonella_aroC.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_config.txt SeqSero2S/seqsero2s_db/kmer/salmonella_dnaN.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_hemD.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_hisD.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_profile.txt SeqSero2S/seqsero2s_db/kmer/salmonella_purE.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_sucA.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_thrA.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_weight.txt SeqSero2S/seqsero2s_db/mlst.pickle SeqSero2S/seqsero2s_db/special.pickle SeqSero2S/setup.py |
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| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b Dockerfile --- a/Dockerfile Fri May 15 17:39:30 2026 +0000 +++ b/Dockerfile Fri May 15 17:50:45 2026 +0000 |
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| b'@@ -1,138 +1,138 @@\n-# Multi-stage Dockerfile for SeqSero2S\n-# Default build: docker build -t seqsero2s:latest .\n-# Test build: docker build --target test -t seqsero2s:test .\n-\n-# ============================================================================\n-# Stage 1: Base image with mambaforge for faster dependency resolution\n-# ============================================================================\n-FROM condaforge/mambaforge:latest AS base\n-\n-LABEL maintainer="SeqSero2S Maintainers"\n-LABEL description="Simplified Salmonella serotype prediction from genome sequencing data"\n-\n-# Set environment variables to reduce conda output and ensure non-interactive\n-# Disable SSL verification for VPN environments\n-ENV CONDA_ALWAYS_YES=true \\\n- CONDA_AUTO_UPDATE_CONDA=false \\\n- DEBIAN_FRONTEND=noninteractive\n-\n-# Configure conda to skip SSL verification\n-RUN conda config --set ssl_verify false\n-\n-# ============================================================================\n-# Stage 2: Builder - Install all dependencies and SeqSero2S\n-# ============================================================================\n-FROM base AS builder\n-\n-# Update base packages and install build essentials\n-RUN apt-get update && \\\n- apt-get install -y --no-install-recommends \\\n- wget \\\n- ca-certificates \\\n- bash \\\n- && apt-get clean && \\\n- rm -rf /var/lib/apt/lists/*\n-\n-# Create conda environment with all dependencies\n-# Using mamba for faster dependency resolution\n-RUN mamba create -n seqsero2s -c conda-forge -c bioconda \\\n- python>=3 \\\n- pip \\\n- setuptools \\\n- blast>=2.2 \\\n- zstd \\\n- samtools \\\n- bedtools>=2.17 \\\n- sra-tools>=2.8 \\\n- spades>=3.9 \\\n- salmid \\\n- bwa>=0.7 \\\n- seqtk>=1.3 \\\n- stringmlst>=0.6 \\\n- mlst>=2.32.2 \\\n- perl-list-moreutils \\\n- && mamba clean -afy\n-\n-# Install SeqSero2S from local fork\n-WORKDIR /tmp/build/SeqSero2S\n-\n-# Copy the current build context (the cloned source code) into the container.\n-COPY . .\n-\n-# Install SeqSero2S\n-RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir\n-\n-# Apply the stringMLST.py patch inline using \'sed\'.\n-# This exactly replicates the original python patch script by commenting out the old line and adding the new one.\n-RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \\\n- sed -i \'s| log = dbPrefix+\'\\\'\'.log\'\\\'\'| # log = dbPrefix+\'\\\'\'.log\'\\\'\'\\n log = os.path.join(os.getcwd(), "kmer.log")|g\' /opt/conda/envs/seqsero2s/bin/stringMLST.py && \\\n- echo "PATCHED: stringMLST.py log path fixed"; \\\n- else \\\n- echo "SKIP: stringMLST.py not found"; \\\n- fi\n-\n-# ============================================================================\n-# Stage 3: Test image - runs validation tests\n-# ============================================================================\n-FROM builder AS test\n-\n-# Create test directory\n-WORKDIR /test\n-\n-# Run test commands from the conda recipe\n-RUN echo "Running SeqSero2S tests..." && \\\n- /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \\\n- echo "SeqSero2S.py -h: PASSED" && \\\n- /opt/conda/envs/seqsero2s/bin/blastn -help && \\\n- echo "blastn -help: PASSED" && \\\n- /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \\\n- echo "SalmID.py -h: PASSED" && \\\n- /opt/conda/envs/seqsero2s/bin/mlst -h && \\\n- echo "mlst -h: PASSED" && \\\n- echo "All tests completed successfully!"\n-\n-# Default command shows test results\n-CMD ["echo", "All SeqSero2S tests passed successfully!"]\n-\n-# ============================================================================\n-# Stage 4: Production/Distribution image - minimal runtime (DEFAULT)\n-# ============================================================================\n-FROM condaforge/mambaforge:latest AS dist\n-\n-# Copy conda environment from builder\n-COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s\n-\n-# Update PATH to use the con'..b'& apt-get clean && \\\r\n+ rm -rf /var/lib/apt/lists/*\r\n+\r\n+# Create conda environment with all dependencies\r\n+# Using mamba for faster dependency resolution\r\n+RUN mamba create -n seqsero2s -c conda-forge -c bioconda \\\r\n+ python>=3 \\\r\n+ pip \\\r\n+ setuptools \\\r\n+ blast>=2.2 \\\r\n+ zstd \\\r\n+ samtools \\\r\n+ bedtools>=2.17 \\\r\n+ sra-tools>=2.8 \\\r\n+ spades>=3.9 \\\r\n+ salmid \\\r\n+ bwa>=0.7 \\\r\n+ seqtk>=1.3 \\\r\n+ stringmlst>=0.6 \\\r\n+ mlst>=2.32.2 \\\r\n+ perl-list-moreutils \\\r\n+ && mamba clean -afy\r\n+\r\n+# Install SeqSero2S from local fork\r\n+WORKDIR /tmp/build/SeqSero2S\r\n+\r\n+# Copy the current build context (the cloned source code) into the container.\r\n+COPY . .\r\n+\r\n+# Install SeqSero2S\r\n+RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir\r\n+\r\n+# Apply the stringMLST.py patch inline using \'sed\'.\r\n+# This exactly replicates the original python patch script by commenting out the old line and adding the new one.\r\n+RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \\\r\n+ sed -i \'s| log = dbPrefix+\'\\\'\'.log\'\\\'\'| # log = dbPrefix+\'\\\'\'.log\'\\\'\'\\n log = os.path.join(os.getcwd(), "kmer.log")|g\' /opt/conda/envs/seqsero2s/bin/stringMLST.py && \\\r\n+ echo "PATCHED: stringMLST.py log path fixed"; \\\r\n+ else \\\r\n+ echo "SKIP: stringMLST.py not found"; \\\r\n+ fi\r\n+\r\n+# ============================================================================\r\n+# Stage 3: Test image - runs validation tests\r\n+# ============================================================================\r\n+FROM builder AS test\r\n+\r\n+# Create test directory\r\n+WORKDIR /test\r\n+\r\n+# Run test commands from the conda recipe\r\n+RUN echo "Running SeqSero2S tests..." && \\\r\n+ /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \\\r\n+ echo "SeqSero2S.py -h: PASSED" && \\\r\n+ /opt/conda/envs/seqsero2s/bin/blastn -help && \\\r\n+ echo "blastn -help: PASSED" && \\\r\n+ /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \\\r\n+ echo "SalmID.py -h: PASSED" && \\\r\n+ /opt/conda/envs/seqsero2s/bin/mlst -h && \\\r\n+ echo "mlst -h: PASSED" && \\\r\n+ echo "All tests completed successfully!"\r\n+\r\n+# Default command shows test results\r\n+CMD ["echo", "All SeqSero2S tests passed successfully!"]\r\n+\r\n+# ============================================================================\r\n+# Stage 4: Production/Distribution image - minimal runtime (DEFAULT)\r\n+# ============================================================================\r\n+FROM condaforge/mambaforge:latest AS dist\r\n+\r\n+# Copy conda environment from builder\r\n+COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s\r\n+\r\n+# Update PATH to use the conda environment\r\n+ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \\\r\n+ CONDA_DEFAULT_ENV=seqsero2s \\\r\n+ CONDA_PREFIX=/opt/conda/envs/seqsero2s\r\n+\r\n+# Install minimal runtime dependencies\r\n+RUN apt-get update && \\\r\n+ apt-get install -y --no-install-recommends \\\r\n+ ca-certificates \\\r\n+ procps \\\r\n+ && apt-get clean && \\\r\n+ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*\r\n+\r\n+# Create working directory\r\n+WORKDIR /data\r\n+\r\n+# Create non-root user for running the application\r\n+RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \\\r\n+ chown -R seqsero2s:seqsero2s /data\r\n+USER seqsero2s\r\n+\r\n+# Add metadata labels\r\n+LABEL org.opencontainers.image.version="1.1.4" \\\r\n+ org.opencontainers.image.authors="LSTUGA" \\\r\n+ org.opencontainers.image.url="https://github.com/LSTUGA/SeqSero2S" \\\r\n+ org.opencontainers.image.documentation="https://github.com/LSTUGA/SeqSero2S" \\\r\n+ org.opencontainers.image.source="https://github.com/LSTUGA/SeqSero2S" \\\r\n+ org.opencontainers.image.licenses="GPL-2.0-or-later" \\\r\n+ org.opencontainers.image.title="SeqSero2S" \\\r\n+ org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data"\r\n+\r\n+# No entrypoint or command for dist target\r\n+\r\n+\r\n' |
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| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/LICENSE Fri May 15 17:50:45 2026 +0000 |
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| b'@@ -0,0 +1,342 @@\n+NOTE: parties interested in commercial licenses should contact the UGA\xe2\x80\x99s Innovation Gateway (https://research.uga.edu/gateway/).\n+\n+\n+GNU GENERAL PUBLIC LICENSE\n+ Version 2, June 1991\n+ \n+ Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>\n+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA\n+ Everyone is permitted to copy and distribute verbatim copies\n+ of this license document, but changing it is not allowed.\n+\n+ Preamble\n+\n+ The licenses for most software are designed to take away your\n+freedom to share and change it. By contrast, the GNU General Public\n+License is intended to guarantee your freedom to share and change free\n+software--to make sure the software is free for all its users. This\n+General Public License applies to most of the Free Software\n+Foundation\'s software and to any other program whose authors commit to\n+using it. 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| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/MANIFEST.in --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/MANIFEST.in Fri May 15 17:50:45 2026 +0000 |
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| @@ -0,0 +1,25 @@ +include LICENSE +include README.md +include MANIFEST.in +include version.py +include setup.py +include seqsero2s_db/antigens.pickle +include seqsero2s_db/H_and_O_and_specific_genes.fasta +include seqsero2s_db/invA_mers_dict +include seqsero2s_db/special.pickle +include seqsero2s_db/mlst.pickle +include seqsero2s_db/kmer/salmonella_35.txt +include seqsero2s_db/kmer/salmonella_aroC.tfa +include seqsero2s_db/kmer/salmonella_config.txt +include seqsero2s_db/kmer/salmonella_dnaN.tfa +include seqsero2s_db/kmer/salmonella_hemD.tfa +include seqsero2s_db/kmer/salmonella_hisD.tfa +include seqsero2s_db/kmer/salmonella.log +include seqsero2s_db/kmer/salmonella_profile.txt +include seqsero2s_db/kmer/salmonella_purE.tfa +include seqsero2s_db/kmer/salmonella_sucA.tfa +include seqsero2s_db/kmer/salmonella_thrA.tfa +include seqsero2s_db/kmer/salmonella_weight.txt +include bin/deinterleave_fastq.sh +include bin/Initial_Conditions_SS2.py +include bin/Initial_Conditions_SS2S.py |
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| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/README.md Fri May 15 17:50:45 2026 +0000 |
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| @@ -0,0 +1,151 @@ +# SeqSero2S + +Salmonella serotype prediction from genome sequencing data. + +Online version: http://www.denglab.info/SeqSero2 + +# Updates since SS2 v1.2.1 +1. Convert the sequences of the following alleles to their reverse complement sequences in the SeqSero2 database. +``` +-fliC_b_Wien_CDC_b,d,j__1488\ +-fliC_d_from-II-48:d:z6_SRR1168371__1521\ +-fliC_a_Salmonella.enterica_from-cdc-Stk2184_other.a__1488 +-fliC_l,v_from-Nchanga_SRR1153349__1503 +-fliC_l,z13,z28_Salmonella.enterica_from-CDC_2011K-0215_l,v__1506 +-fljB_1,7_Salmonella.enterica_from-cdc_Stk1415_1__1521 +-fljB_1,5_from-cdc_Stk2184_1__1521 +-fljB_1,5_from-Infantis-micro-assembly_SRR1106258_1__1521 +-fljB_z6_from-II-48:d:z6_SRR1168371__1503 +``` +2. Delete the following alleles from the SeqSero2 database because of the existence of mutations. +``` +-fliC_y_Bareillystr_AOZP01000027_other.y__1508 +-fliC_d_Muenchenstr_ARYW01000085_b,d,j__1496 +-fliC_d_Muenchenstr_ARYX01000110_b,d,j__1488 +-fliC_g,m_Enteritidisstr_ALHD01000038_g,m__1507 +-fljB_1,2_Newportstr_AYDZ01000021_1__1510 +``` +2. Add a fliC 1,5,7 allele and a fliC 1,2,7 allele into the SeqSero2 database. +``` +-fliC_1,5,7_Salmonella.enterica_from-cdc-Stk1778_1,5,7_1521 +-fliC_1,2,7_Salmonella.enterica_from-cdc-Stk2293_1,2,7_1521 +``` +3. Delete the O54 allele +``` +-O-54_wbbF__1380 +``` +4. Fixed the bug that caused the misidentification of O9 and O2 by the micro-assembly workflow +5. Update serotype names based on the simplified KWS scheme +6. Remove the 9,46,27 allele +``` +-O-9,46,27_partial_wzy__1019 +``` +7. Remove two fljB_1,2 allels +``` +-fljB_1,2_from-Brazzaville_SRR2058145_1__1521 +-fljB_1,2_Salmonella.enterica_1,4,5,12:i:1,2,7_AY353272_1__1521 +``` +8. Run 7-gene MLST analysis using stringMLST/mlst + +# Introduction +SeqSero2S is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies + +# Dependencies +SeqSero2S has three workflows: + +(A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). + +Allele micro-assembly workflow depends on: + +1. Python 3; +2. Biopython 1.73; +3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); +4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); +5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); +6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); +7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); +8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); +9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID); +10. [stringMLST v0.6.3](https://github.com/jordanlab/stringMLST); + +(B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. + +Raw reads k-mer workflow (originally SeqSeroK) depends on: + +1. Python 3; +2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); +3. [mlst v2.22.1](https://github.com/tseemann/mlst). + + +(C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow + +# Installation +### Git +Install mlst and stringMLST first +``` +conda install mlst +``` +``` +pip install stringMLST +``` +To install the SeqSero2S git repository locally: +``` +git clone https://github.com/LSTUGA/SeqSero2S.git +cd SeqSero2S +python3 -m pip install --user . +``` + +# Executing the code +Make sure all SeqSero2S and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2S.py to get detailed instructions. + + Usage: SeqSero2S.py + + -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore reads (fasta/fastq)) + + -i <file> (/path/to/input/file) + + -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) + + -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c <flag> (if '-c' was flagged, SeqSero2S will only output serotype prediction without the directory containing log files) + + -n <string> (optional, to specify a sample name in the report output) + + -s <flag> (if '-s' was flagged, SeqSero2S will not output header in SeqSero_result.tsv) + + --check <flag> (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + +# Examples +Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2S.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + +K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2S.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2S.py -m k -t 4 -i assembly.fasta + +# Output +Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + +# Citation +Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. +SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. +**Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + +Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. +Salmonella serotype determination utilizing high-throughput genome sequencing data. +**J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/bin/Initial_Conditions_SS2.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/bin/Initial_Conditions_SS2.py Fri May 15 17:50:45 2026 +0000 |
| [ |
| b"@@ -0,0 +1,109 @@\n+#!/usr/bin/env python\n+\n+subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'VI', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 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'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun']\n+\n+rename_dict={'Nitra': 'Enteritidis',\n+ 'Kiel': 'Dublin',\n+ 'Koessen': 'Panama',\n+ 'Phaliron': 'Kalumburu',\n+ 'Istanbul': 'Hadar',\n+ 'Haardt': 'Blockley',\n+ 'Ferruch': 'Kottbus',\n+ 'Sanga': 'Eboko',\n+ 'Pakistan': 'Litchfield',\n+ 'Bellevue': 'Lezennes',\n+ 'Sunnycove': 'Daarle',\n+ 'Noya': 'Akanji',\n+ 'Virginia': 'Muenchen',\n+ 'Djelfa': 'Skansen',\n+ 'Konstanz': 'Gatuni',\n+ 'Bardo': 'Newport',\n+ 'Houston': 'Panama',\n+ 'Martonos': 'Finkenwerder',\n+ 'Midway': 'Florida',\n+ 'Lindern': 'Charity',\n+ 'Bahrenfeld': 'Onderstepoort',\n+ 'Schalkwijk': 'Moussoro',\n+ 'Amberg': 'Boecker',\n+ 'Madelia': 'Carrau',\n+ 'Soahanina': 'Sundsvall',\n+ 'Stafford': 'Poano',\n+ 'Chichiri': 'Uzaramo',\n+ 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]',\n+ 'Hindmarsh':'Bovismorbificans',\n+ 'Yovokome': 'Manhattan'}\n+\n+ #potential merge for O22 and O23\n+ #'Ibadan': 'Mississippi',\n+ #'Bracknell': 'Oudwijk',\n+ #'Vaertan': 'Ullevi',\n+ #'Bahati': 'Durham',\n+ #'Wichita': 'Friedenau',\n+ #'Diguel': 'Telelkebir',\n+ #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5',\n+ #'Washington': 'Kintambo',\n+ #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39',\n+ #'Serenli': 'Winslow',\n+ #'Farmsen': 'Poona',\n+ #'Durance': 'Ivrysurseine',\n+ #'Agoueve': 'Cubana',\n+ #'II 13,23:z29:1,5': 'II 13,22:z29:1,5',\n+ #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x',\n+ #'Picpus': 'Mampong',\n+ #'Anna': 'Nimes',\n+ #'Fanti': 'Leiden',\n+ #'Ried': 'Ajiobo',\n+\n+ #potential O68 list\n+ #'Djelfa': 'Skansen',\n+ #'Korbol': 'Nagoya',\n+ #'Sanga': 'Eboko',\n+ #'Konstanz': 'Gatuni',\n+ #'Presov': 'Shipley',\n+ #'Heistopdenberg': 'Bukuru',\n+ #'Tounouma': 'Banalia',\n+ #'Gaillac': 'Utah',\n+ #'Santiago': 'Belem',\n+ #'Virginia': 'Muenchen',\n+ #'Yovokome': 'Manhattan',\n+ #'Portanigra': 'Dunkwa',\n+ #'Bardo': 'Newport',\n+ #'Ferruch': 'Kottbus',\n+ #'Alminko': 'Nanergou',\n+ #'Bargny': 'Takoradi',\n+ #'Magherafelt': 'Cyprus',\n+ #'Haardt': 'Blockley',\n+ #'Pakistan': 'Litchfield',\n+ #'Yokoe': 'Bassa',\n+ #'Noya': 'Akanji',\n+ #'Lamphun': 'Giza',\n+ #'Tananarive': 'Brunei',\n+ #'Inchpark': 'Alagbon',\n+ #'Sunnycove': 'Daarle',\n+ #'Sindelfingen': 'Benue',\n+ #'Phaliron': 'Kalumburu',\n+ #'Bazenheid': 'Zerifin',\n+ #'Paris': 'Mapo',\n+ #'Istanbul': 'Hadar',\n+ #'Chomedey': 'Glostrup',\n+ #'Wippra': 'Molade',\n+ #'Uno': 'Tamale',\n+ #'Kolda': 'Yarm',\n+ #'Bellevue': 'Lezennes',\n+ #'Albany':'Duesseldorf'\n" |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/bin/Initial_Conditions_SS2S.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/bin/Initial_Conditions_SS2S.py Fri May 15 17:50:45 2026 +0000 |
| [ |
| b"@@ -0,0 +1,110 @@\n+#!/usr/bin/env python\n+\n+subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'VI', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 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'I', 'I', 'I', 'II', 'I', 'I', 'IIIb', 'I', 'I', 'IIIb', 'IIIb', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'IIIb', 'IIIb', 'IIIb', 'I', 'I', 'I', 'I', 'IIIb', 'IIIb', 'I', 'I', 'I', 'II', 'IIIb', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'IIIb', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'IV', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'bongori', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I"..b"0:m,t:z42', 'II 40:z:z42', 'II [1],40:z42:1,6', 'II 43:b:z42', 'II 43:d:z42', 'II 43:z29:z42', 'II 43:z42:[1,5,7]', 'II 44:g,t:z42', 'II [1],44:m,t:z42', 'II 45:z29:z42', 'II 50:l,z28:z42', 'II 50:z42:1,7', 'II 53:d:z42', 'II 57:a:z42', 'II 57:z29:z42', 'II 57:z42:1,6:z53', 'II 3,10:z38:z42', 'II 1,6,14:z42:1,6', 'IIIb 18:(k):z54', 'IIIb 47:l,v:z57', 'IIIb 50:l,v:z57', 'IIIb 38:(k):z55', 'IIIb 21:l,v:z57', 'IIIb 48:k:z57', 'IIIb 59:z10:z57', 'IIIb 42:z57:1,5', 'Aesch', 'IIIb 38:z61:[z53]', 'Oakey', 'Aarhus', 'Franken', 'IIIb 42:z10:z67', 'VI 50:l,v:z67', 'IIIb 53:r:z68', 'Delmenhorst', 'II 3,15:z87:e,n,x,z15', 'VI 6,14:l,v:z88', 'Mygdal', 'II 1,9,12,46,27:a:z6', 'II 1,9,12,46,27:b:z39', 'II 1,9,12,46,27:c:z39', 'II 9,12,46,27:g,t:e,n,x', 'II 1,9,12,46,27:l,z13,z28:z39', 'II 1,9,12,46,27:y:z39', 'II 1,9,12,46,27:z10:1,5', 'II 1,9,12,46,27:z10:e,n,x', 'II 1,9,12,46,27:z10:z39', 'II 1,9,12,46,27:z4,z24:1,5', 'Tonev', 'Winnipeg', 'Rossleben', 'Borreze', 'Uccle', 'Poeseldorf', 'Ochsenwerder', 'Newholland', 'Czernyring', 'Steinwerder', 'Canton', 'Barry', 'Mundubbera', 'Yerba', 'Sendai', 'Abortusequi']\n+\n+rename_dict={\n+ 'Nitra': 'Enteritidis',\n+ 'Kiel': 'Dublin',\n+ 'Koessen': 'Panama',\n+ 'Phaliron': 'Kalumburu',\n+ 'Istanbul': 'Hadar',\n+ 'Haardt': 'Blockley',\n+ 'Ferruch': 'Kottbus',\n+ 'Eboko': 'Sanga',\n+ 'Pakistan': 'Litchfield',\n+ 'Bellevue': 'Lezennes',\n+ 'Daarle': 'Sunnycove',\n+ 'Noya': 'Akanji',\n+ 'Virginia': 'Muenchen',\n+ 'Skansen': 'Djelfa',\n+ 'Konstanz': 'Gatuni',\n+ 'Bardo': 'Newport',\n+ 'Houston': 'Panama',\n+ 'Martonos': 'Finkenwerder',\n+ 'Midway': 'Florida',\n+ 'Lindern': 'Charity',\n+ 'Bahrenfeld': 'Onderstepoort',\n+ 'Moussoro': 'Schalkwijk',\n+ 'Amberg': 'Boecker',\n+ 'Madelia': 'Carrau',\n+ 'Soahanina': 'Sundsvall',\n+ 'Stafford': 'Poano',\n+ 'Chichiri': 'Uzaramo',\n+ 'Hindmarsh':'Bovismorbificans',\n+ 'Yovokome': 'Manhattan',\n+ ## SS2S\n+ 'Fulica': 'I 4:a:-',\n+ 'Korbol': 'Nagoya',\n+ 'Presov': 'Shipley',\n+ 'Heistopdenberg': 'Bukuru',\n+ 'Tounouma': 'Banalia',\n+ 'Gaillac': 'Utah',\n+ 'Santiago': 'Belem',\n+ 'Portanigra': 'Dunkwa',\n+ 'Alminko': 'Nanergou',\n+ 'Bargny': 'Takoradi',\n+ 'Magherafelt': 'Cyprus',\n+ 'Bassa': 'Yokoe',\n+ 'Lamphun': 'Giza',\n+ 'Brunei': 'Tananarive',\n+ 'Inchpark': 'Alagbon',\n+ 'Sindelfingen': 'Benue',\n+ 'Bazenheid': 'Zerifin',\n+ 'Paris': 'Mapo',\n+ 'Chomedey': 'Glostrup',\n+ 'Wippra': 'Molade',\n+ 'Uno': 'Tamale',\n+ 'Kolda': 'Yarm',\n+ 'Duesseldorf': 'Albany',\n+ 'Rosenberg': 'Enteritidis',\n+ 'Blegdam': 'Enteritidis',\n+ 'Moscow': 'Enteritidis',\n+ 'Antarctica': 'Enteritidis',\n+ #'Chincol': 'Emek',\n+ 'Dessau': 'Senftenberg',\n+ 'Naestved': 'Dublin',\n+ 'Rostock': 'Dublin',\n+ ##update names\n+ 'IIIb 6,7:(k):z': 'IIIb 7:k:z',\n+ 'IIIb 16:(k):e,n,x,z15': 'IIIb 16:k:e,n,x,z15',\n+ 'IIIb 60:i:[e,n,x,z15]': 'IIIb 60:i:e,n,x,z15',\n+ 'IIIb 60:i:[z]': 'IIIb 60:i:z',\n+ 'IIIb 60:i:[z35]': 'IIIb 60:i:z35',\n+ 'II [1],13,22:g,m,t:[1,5]': 'II 13,22:g,m,t:1,5',\n+ 'II 6,7:z29:[z42]': 'II 7:z29:-',\n+ 'II [1],13,22:g,t:[1,5]': 'II 13,22:g,t:1,5',\n+ 'II 16:m,t:[z42]': 'II 16:m,t:-',\n+ 'II 17:g,t:[e,n,x,z15]': 'II 17:g,t:e,n,x,z15',\n+ 'VI 1,6,14,25:z10:1,(2),7': 'VI 6,14:z10:1,2,7',\n+ 'II 13,22:m,t:z42:z39': 'II 13,22:m,t:z39',\n+}\n+\n+#potential merge for O22 and O23\n+ #'Ibadan': 'Mississippi',\n+ #'Bracknell': 'Oudwijk',\n+ #'Vaertan': 'Ullevi',\n+ #'Bahati': 'Durham',\n+ #'Wichita': 'Friedenau',\n+ #'Diguel': 'Telelkebir',\n+ #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5',\n+ #'Washington': 'Kintambo',\n+ #'Winslow': 'Serenli',\n+ #'Farmsen': 'Poona',\n+ #'Ivrysurseine': 'Durance',\n+ #'Agoueve': 'Cubana',\n+ #'II [1],13,23:z29:1,5': 'II 13,22:z29:1,5',\n+ #'II [1],13,23:z29:e,n,x': 'II 13,22:z29:e,n,x',\n+ #'Picpus': 'Mampong',\n+ #'Nimes': 'Anna',\n+ #'Fanti': 'Leiden',\n+ #'Ried': 'Ajiobo',\n" |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/bin/SeqSero2S.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/bin/SeqSero2S.py Fri May 15 17:50:45 2026 +0000 |
| [ |
| b'@@ -0,0 +1,1723 @@\n+#!/usr/bin/env python3\n+\n+import sys\n+import time\n+import random\n+import os\n+import subprocess\n+import gzip\n+import io\n+import pickle\n+import argparse\n+import itertools\n+import json\n+from distutils.version import LooseVersion\n+from distutils.spawn import find_executable\n+sys.path.insert(1,sys.path[0]+\'/..\')\n+\n+__version__ = "1.1.4"\n+\n+### SeqSero Kmer\n+def parse_args():\n+ "Parse the input arguments, use \'-h\' for help."\n+ parser = argparse.ArgumentParser(usage=\'SeqSero2S.py -t <data_type> -m <mode> -i <input_data> [-d <output_directory>] [-p <number of threads>] [-b <BWA_algorithm>]\\n\\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\\n\\nContact email:seqsero@gmail.com\\n\\n\')#add "-m <data_type>" in future\n+ parser.add_argument("-i",nargs="+",help="<string>: path/to/input_data",type=os.path.abspath) ### add \'type=os.path.abspath\' to generate absolute path of input data.\n+ parser.add_argument("-t",choices=[\'1\',\'2\',\'3\',\'4\',\'5\'],help="<int>: \'1\' for interleaved paired-end reads, \'2\' for separated paired-end reads, \'3\' for single reads, \'4\' for genome assembly, \'5\' for nanopore reads (fasta/fastq)")\n+ parser.add_argument("-b",choices=[\'sam\',\'mem\'],default="mem",help="<string>: algorithms for bwa mapping for allele mode; \'mem\' for mem, \'sam\' for samse/sampe; default=mem; optional; for now we only optimized for default \'mem\' mode")\n+ parser.add_argument("-p",default="1",help="<int>: number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1")\n+ parser.add_argument("-m",choices=[\'k\',\'a\'],default="a",help="<string>: which workflow to apply, \'a\'(raw reads allele micro-assembly), \'k\'(raw reads and genome assembly k-mer), default=a")\n+ parser.add_argument("-n",help="<string>: optional, to specify a sample name in the report output")\n+ parser.add_argument("-d",help="<string>: optional, to specify an output directory name, if not set, the output directory would be \'SeqSero_result_\'+time stamp+one random number")\n+ parser.add_argument("-c",action="store_true",help="<flag>: if \'-c\' was flagged, SeqSero2S will only output serotype prediction without the directory containing log files")\n+ parser.add_argument("-s",action="store_true",help="<flag>: if \'-s\' was flagged, SeqSero2S will not output header in SeqSero_result.tsv")\n+ parser.add_argument("--phred_offset",choices=[\'33\',\'64\',\'auto\'],default=\'auto\',help="<33|64|auto>: offset for FASTQ file quality scores, default=auto")\n+ parser.add_argument("--check",action="store_true",help="<flag>: use \'--check\' flag to check the required dependencies")\n+ parser.add_argument(\'-v\', \'--version\', action=\'version\', version=f"%(prog)s {__version__}")\n+ return parser.parse_args()\n+\n+### check paths of dependencies\n+check_dependencies = parse_args().check\n+dependencies = [\'bwa\',\'samtools\',\'blastn\',\'fastq-dump\',\'spades.py\',\'bedtools\',\'SalmID.py\',\'mlst\',\'stringMLST.py\']\n+if check_dependencies:\n+ for item in dependencies:\n+ ext_path = find_executable(item)\n+ if ext_path is not None:\n+ print ("Using "+item+" - "+ext_path)\n+ else:\n+ print ("ERROR: can not find "+item+" in PATH")\n+ sys.exit()\n+### end of --check\n+\n+def reverse_complement(sequence):\n+ complement = {\n+ \'A\': \'T\',\n+ \'C\': \'G\',\n+ \'G\': \'C\',\n+ \'T\': \'A\',\n+ \'N\': \'N\',\n+ \'M\': \'K\',\n+ \'R\': \'Y\',\n+ \'W\': \'W\',\n+ \'S\': \'S\',\n+ \'Y\': \'R\',\n+ \'K\': \'M\',\n+ \'V\': \'B\',\n+ \'H\': \'D\',\n+ \'D\': \'H\',\n+ \'B\': \'V\'\n+ }\n+ return "".join(complement[base] for base in reversed(sequence))\n+\n+def mlst(assembly):\n+ subprocess.check_call("mlst -q --json mlst.json --scheme senterica_achtman_2 "+assembly+" >> data_log.txt 2>&1",shell=True)\n+ f = open("mlst.json",\'r\')\n+ mlst_result = json.load(f)\n+ f.close()\n+'..b'"\\n"+\n+ "O antigen prediction:\\t"+O_choice+"\\n"+\n+ "H1 antigen prediction(fliC):\\t"+highest_fliC+"\\n"+\n+ "H2 antigen prediction(fljB):\\t"+highest_fljB+"\\n"+\n+ "Predicted identification:\\t"+subspecies_ID_dir[ssp_pointer]+"\\n"+\n+ "Predicted antigenic profile:\\t"+predict_form+"\\n"+\n+ "Predicted serotype:\\t"+predict_sero+"\\n"+\n+ "Predicted serotype (SeqSero2 v1.3.2):\\t"+predict_sero_ss2+"\\n"+\n+ note+star_line+claim+antigen_note+"\\n")#+##\n+ tsv_file.write(make_dir+"\\t"+input_file+"\\t"+O_choice+"\\t"+highest_fliC+"\\t"+highest_fljB+"\\t"+subspecies_ID_dir[ssp_pointer]+"\\t"+predict_form+"\\t"+predict_sero+"\\t"+predict_sero_ss2+"\\t"+star_line+claim+antigen_note+"\\t"+st+"\\n")\n+ else:\n+ new_file.write("Output directory:\\t"+make_dir+"\\n"+\n+ "Input files:\\t"+input_file+"\\n"+\n+ "O antigen prediction:\\t"+O_choice+"\\n"+\n+ "H1 antigen prediction(fliC):\\t"+highest_fliC+"\\n"+\n+ "H2 antigen prediction(fljB):\\t"+highest_fljB+"\\n"+\n+ "Predicted identification:\\t"+subspecies_ID_dir[ssp_pointer]+"\\n"+\n+ "Predicted antigenic profile:\\t"+predict_form+"\\n"+\n+ "Predicted serotype:\\t"+subspecies+\' \'+predict_form+"\\n"+ # add serotype output for "N/A" prediction, subspecies\n+ "Predicted serotype (SeqSero2 v1.3.2):\\t"+subspecies+\' \'+predict_form_ss2+"\\n"+\n+ note+NA_note+star_line+claim+antigen_note+"\\n")#+##\n+ tsv_file.write(make_dir+"\\t"+input_file+"\\t"+O_choice+"\\t"+highest_fliC+"\\t"+highest_fljB+"\\t"+subspecies_ID_dir[ssp_pointer]+"\\t"+predict_form+"\\t"+subspecies+\' \'+predict_form+"\\t"+subspecies+\' \'+predict_form_ss2+"\\t"+NA_note+star_line+claim+antigen_note+"\\t"+st+"\\n")\n+ ###MLST\n+ new_file.write("Sequence type:\\t"+st+"\\n"+\n+ "Number of ST"+st+" strains in EnteroBase:\\t"+st_count+"\\n"+\n+ "\\n".join([k+":\\t"+v for k,v in sorted_alleles]))\n+ ###\n+ new_file.close()\n+ tsv_file.close()\n+ if "N/A" not in predict_sero:\n+ print("Output directory:\\t"+make_dir+"\\n"+\n+ "Input files:\\t"+input_file+"\\n"+\n+ "O antigen prediction:\\t"+O_choice+"\\n"+\n+ "H1 antigen prediction(fliC):\\t"+highest_fliC+"\\n"+\n+ "H2 antigen prediction(fljB):\\t"+highest_fljB+"\\n"+\n+ "Predicted identification:\\t"+subspecies_ID_dir[ssp_pointer]+"\\n"+\n+ "Predicted antigenic profile:\\t"+predict_form+"\\n"+\n+ "Predicted serotype:\\t"+predict_sero+"\\n"+\n+ "Predicted serotype (SeqSero2 v1.3.2):\\t"+predict_sero_ss2+"\\n"+\n+ note+star_line+claim+antigen_note+"\\n")#+##\n+ else:\n+ print("Output directory:\\t"+make_dir+"\\n"+\n+ "Input files:\\t"+input_file+"\\n"+\n+ "O antigen prediction:\\t"+O_choice+"\\n"+\n+ "H1 antigen prediction(fliC):\\t"+highest_fliC+"\\n"+\n+ "H2 antigen prediction(fljB):\\t"+highest_fljB+"\\n"+\n+ "Predicted identification:\\t"+subspecies_ID_dir[ssp_pointer]+"\\n"+\n+ "Predicted antigenic profile:\\t"+predict_form+"\\n"+\n+ "Predicted serotype:\\t"+subspecies+\' \'+predict_form+"\\n"+ # add serotype output for "N/A" prediction, subspecies\n+ "Predicted serotype (SeqSero2 v1.3.2):\\t"+subspecies+\' \'+predict_form_ss2+"\\n"+\n+ note+NA_note+star_line+claim+antigen_note+"\\n")#+##\n+ ###MLST\n+ print("Sequence type: "+st)\n+ print("Number of ST"+st+" strains in EnteroBase: "+st_count)\n+ #print("Allele profile...")\n+ for k,v in sorted_alleles:\n+ print(k+\': \'+v)\n+ print(\'\\n\')\n+ ###\n+if __name__ == \'__main__\':\n+ main()\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/bin/SeqSero2_update_kmer_database.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/bin/SeqSero2_update_kmer_database.py Fri May 15 17:50:45 2026 +0000 |
| [ |
| @@ -0,0 +1,113 @@ +#!/usr/bin/env python3 + +import argparse +import os,subprocess +import pickle + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') + return parser.parse_args() + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + +def multifasta_to_kmers_dict(multifasta): + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) + return lib_dict + +def get_salmid_invA_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/invA_mers_dict', 'rb') + invA_dict = pickle.load(a) + try: + del invA_dict['version'] + except: + pass + return invA_dict + +def get_salmid_rpoB_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/rpoB_mers_dict', 'rb') + rpoB_dict = pickle.load(a) + try: + del rpoB_dict['version'] + except: + pass + return rpoB_dict + +def main(): + args = parse_args() + ex_dir = os.path.dirname(os.path.realpath(__file__)) + lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') + invA_dict=get_salmid_invA_database(ex_dir) + #rpoB_dict=get_salmid_rpoB_database(ex_dir) + lib_dict_new = lib_dict.copy() + #print(len(lib_dict_new)) + lib_dict_new.update(invA_dict) + #print(len(lib_dict_new)) + #lib_dict_new.update(rpoB_dict) + #print(len(lib_dict_new)) + f = open(ex_dir + '/antigens.pickle', "wb") + pickle.dump(lib_dict_new, f) + f.close() + +if __name__ == '__main__': + main() |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/bin/deinterleave_fastq.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/bin/deinterleave_fastq.sh Fri May 15 17:50:45 2026 +0000 |
| [ |
| @@ -0,0 +1,30 @@ +#!/bin/bash +# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] +# +# Deinterleaves a FASTQ file of paired reads into two FASTQ +# files specified on the command line. Optionally GZip compresses the output +# FASTQ files using pigz if the 3rd command line argument is the word "compress" +# +# Can deinterleave 100 million paired reads (200 million total +# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) +# +# Latest code: https://gist.github.com/3521724 +# Also see my interleaving script: https://gist.github.com/4544979 +# +# Inspired by Torsten Seemann's blog post: +# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html + +# Set up some defaults +GZIP_OUTPUT=0 +PIGZ_COMPRESSION_THREADS=10 + +# If the third argument is the word "compress" then we'll compress the output using pigz +if [[ $3 == "compress" ]]; then + GZIP_OUTPUT=1 +fi + +if [[ ${GZIP_OUTPUT} == 0 ]]; then + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 +else + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 +fi |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/H_and_O_and_specific_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/H_and_O_and_specific_genes.fasta Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,6923 @@\n+>fliC_g,m_Enteritidisstr_AKFY01000033_g,m__1506\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC\n+CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT\n+TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT\n+GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC\n+CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG\n+GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG\n+CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA\n+ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG\n+CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA\n+AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT\n+TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA\n+ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT\n+AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA\n+AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG\n+AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA\n+AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC\n+AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG\n+TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG\n+ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT\n+>fliC_g,m,s_Montevideostr_AESV01000018_g,m__1506\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC\n+CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT\n+TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC\n+GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC\n+CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG\n+GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG\n+CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA\n+ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG\n+CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA\n+AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT\n+TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA\n+ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT\n+AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA\n+AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG\n+AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT\n+AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC\n+AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG\n+TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG\n+ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT\n+>fljB_1,2_Salmonella.enterica_Stanley_AY353267_1__1521\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC\n+CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT\n+TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC\n+GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC\n+TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG\n+GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG\n+AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC\n+AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG\n+GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT'..b'CGGTGACAATGACCGCAAATAAATCAACAGTAACTGGGGCCGG\n+CACAGTTACCAAAAACCAAATTGTAGACGCTGTTACTCCGGCACCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCA\n+ATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGAT\n+GCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAGACTGGTGAGATAAAAGCTAAGAC\n+TGTAAATTATACTGACGCTACTGGTGCAACAAAAACTGGTGCTGTGAAATTTGGCGGCGCGAATGGTAAAACTGAAGTTG\n+TGACTACAGTTGATGGTAATACTTATCAGGCTAGTGATGTGAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGTGAG\n+GCTGTGACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCT\n+GGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAATCTGGGCAATACCGTAAACAACTTGTCTGAAGCGCGTAGCC\n+GTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTT\n+CTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\n+>fliC_1,5,7_Salmonella.enterica_from-cdc-Stk1778_1,5,7__1521\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC\n+TGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT\n+TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC\n+GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC\n+TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG\n+GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTG\n+AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC\n+AACGACAGCTTATGCCGATAACGGTACTACATTGAATGTCTCAGGCCTTGATGATGCAGCTATCAAAGCGGCTACGGGGG\n+GTACGACTGGTGCACCTACTGTAACAGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG\n+GGCTTTACTGGTGGTGATCTCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACACTTGCGCC\n+TGGTGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAACTACACCGGTAGCTG\n+CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG\n+TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGCTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA\n+CGACGAAACGACAGGGGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACAGCGGCTAACC\n+AACTGGGTGGCGCAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT\n+GATTTCAAAGCACAGCCAGAGCTGGCGGAAGCGGCTGCTAAAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCT\n+GGCGCAGGTGGATGCACTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA\n+CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG\n+CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA\n+A\n+>fliC_1,2,7_Salmonella.enterica_from-cdc-Stk2293_1,2,7__1521\n+ATGGCACAAGTCATTAACACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC\n+TGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT\n+TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC\n+GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC\n+TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG\n+GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG\n+AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC\n+AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG\n+GTACGAATGGTGCACCTGCTGTAACAGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT\n+GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACACTTGCGCC\n+TGGTGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGCTACACCGGTAGCTG\n+CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGGCGCTGAGTTGGTCAAAATG\n+TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGCTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA\n+CGACGAAACGACAGGGGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACAGCGGCTAACC\n+AACTGGGTGGCGCAGACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCAC\n+AACTTCAAAGCACAGCCAGAGCTGGCTGAAGTAGCTACTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCT\n+GGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA\n+CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG\n+CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA\n+A\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/antigens.pickle |
| b |
| Binary file SeqSero2S/seqsero2s_db/antigens.pickle has changed |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/invA_mers_dict |
| b |
| Binary file SeqSero2S/seqsero2s_db/invA_mers_dict has changed |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella.log Fri May 15 17:50:45 2026 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +06/26/2023 09:03:06 AM singleSampleTool : GDUTNS--Y1.R1.raw.fastq.gz and GDUTNS--Y1.R2.raw.fastq.gz +06/26/2023 09:03:06 AM singleSampleTool : paired True +06/26/2023 09:03:06 AM singleSampleTool : fastq1 start +06/26/2023 09:03:06 AM singleFileTool :GDUTNS--Y1.R1.raw.fastq.gz +06/26/2023 09:03:06 AM singleFileTool : fastq +06/26/2023 09:03:06 AM fileExplorer :GDUTNS--Y1.R1.raw.fastq.gz +06/26/2023 09:03:54 AM singleSampleTool : fastq1 done +06/26/2023 09:03:54 AM singleSampleTool : fastq2 start +06/26/2023 09:03:54 AM singleFileTool :GDUTNS--Y1.R2.raw.fastq.gz +06/26/2023 09:03:54 AM singleFileTool : fastq +06/26/2023 09:03:54 AM fileExplorer :GDUTNS--Y1.R2.raw.fastq.gz +06/26/2023 09:04:48 AM singleSampleTool : fastq2 done +06/26/2023 09:04:48 AM singleSampleTool : weightedProfile start +06/26/2023 09:04:48 AM weightedProf +06/26/2023 09:04:48 AM singleSampleTool : weightedProfile finished +06/26/2023 09:04:48 AM singleSampleTool : getMaxCount start +06/26/2023 09:04:48 AM getMaxCount +06/26/2023 09:04:48 AM Max Support :GDUTNS--Y : {'purE': {'5': 54640}, 'dnaN': {'8': 75064}, 'thrA': {'15': 80816}, 'sucA': {'11': 61141}, 'hemD': {'11': 72516}, 'aroC': {'8': 77112}, 'hisD': {'11': 51911}} +06/26/2023 09:04:48 AM Second Max Support :GDUTNS--Y : {'purE': {'4': 48207, '456': 48207}, 'dnaN': {'1': 58680, '492': 58680}, 'thrA': {'10': 63003}, 'sucA': {'9': 58437, '46': 58437, '109': 58437, '197': 58437, '413': 58437, '570': 58437, '925': 58437, '1060': 58437}, 'hemD': {'3': 65987}, 'aroC': {'7': 67451}, 'hisD': {'1': 40164, '353': 40164}} +06/26/2023 09:04:48 AM singleSampleTool : getMaxCount end +06/26/2023 09:04:48 AM singleSampleTool : findST start +06/26/2023 09:04:48 AM findST +06/26/2023 09:04:48 AM singleSampleTool : findST end +06/26/2023 09:04:48 AM Command :['/home/shaoting/.conda/envs/seqsero2s/bin/stringMLST.py', '--predict', '-P', 'kmer/salmonella', '-1', 'GDUTNS--Y1.R1.raw.fastq.gz', '-2', 'GDUTNS--Y1.R2.raw.fastq.gz', '-o', 'GDUTNS--Y1_stringMLST.txt'] |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_35.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_35.txt Fri May 15 17:50:45 2026 +0000 |
| [ |
| b'@@ -0,0 +1,388076 @@\n+GTTTTTCGCCCGGGACACGCGGATTACACCTATGA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TCATAGGTGTAATCCGCGTGTCCCGGGCGAAAAAC\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TTTTTCGCCCGGGACACGCGGATTACACCTATGAG\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+CTCATAGGTGTAATCCGCGTGTCCCGGGCGAAAAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TTTTCGCCCGGGACACGCGGATTACACCTATGAGC\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+GCTCATAGGTGTAATCCGCGTGTCCCGGGCGAAAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TTTCGCCCGGGACACGCGGATTACACCTATGAGCA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TGCTCATAGGTGTAATCCGCGTGTCCCGGGCGAAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TTCGCCCGGGACACGCGGATTACACCTATGAGCAG\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+CTGCTCATAGGTGTAATCCGCGTGTCCCGGGCGAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TCGCCCGGGACACGCGGATTACACCTATGAGCAGA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TCTGCTCATAGGTGTAATCCGCGTGTCCCGGGCGA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+CGCCCGGGACACGCGGATTACACCTATGAGCAGAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TTCTGCTCATAGGTGTAATCCGCGTGTCCCGGGCG\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+GCCCGGGACACGCGGATTACACCTATGAGCAGAAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+TTTCTGCTCATAGGTGTAATCCGCGTGTCCCGGGC\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+CCCGGGACACGCGGATTACACCTATGAGCAGAAAT\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+ATTTCTGCTCATAGGTGTAATCCGCGTGTCCCGGG\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n+CCGGGACACGCGGATTACACCTATGAGCAGAAATA\taroC\t[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,27,28,29,30,31,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,50,51,52,53,56,59,60,61,62,63,65,67,68,69,70,72,75,76,77,78,79,80,81,82,87,88,89,90,92,93,94,98,99,100,101,102,103,105,106,107,108,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,128,129,130,131,136,137,140,141,142,143,144,147,148,150,152,153,154,155,156,158,159,160,161,162,163,164,165,168,169,170,172,175,178,179,182,183,184,185,186,187,189,193,194,195,196,197,198,199,200,201,202,203,208,209,210,213,214,215,218,221,222,225,230,231,232,233,234,244,250,254,255,256,261,262,270,277,279,282,289,290,291,294,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,315,316,319,320,321,322,324,325,326,328,329,331,332,333,336,338,341,342,343,344,345,346,347,348,349,351,353,355,357,359,360,361,362,363,364,365,367,368,369,371,373,374,375,376,379,381,382,383,386,391,397,398,400,401,403,404,407,408,409,410,411,412,413,415,416,418,419,420,421,426,428,430,431,434,435,437,438,439,440,441,442,443,444,450,451,453,454,457,462,463,464,465,468,470,472,473,474,475,476,478,480,481,482,483,484,485,488,490,492,493,494,495,496,497,498,501,504,505,507,509,511,512,514,515,519,520,523,526,527,528,529,530,531,532,533,534,535,536,537,538,540,541,542,543,544,545,546,547,548,549,551,553,558,559,560,561,564,565,566,567,568,569,571,572,575,576,579,581,582,583,584,587,589,590,592,594,595,597,599,601,602,604,608,626,627,628,630,631,634,636,640,641,646,647,650,651,652,653,658,660,662,663,664,665,666,667,668,669,670,672,673,674,675,678,679,680,681,686,688,691,692,693,698,699,700,701,702,706,711,713,717,718,719,720,723,724,725,726,727,729,732,733,734,735,736,739,740,742,747,748,749,750,751,752,753,755,756,757,759,760,761,763,764,765,766,767,770,771,773,774,776,778,779,781,782,783,784,785,786,787,788,789,790,791,792,794,795,796,799,800,801,804,805,808,809,810,811,812,814,816,818,820,821,822,823,825,826,827,830,831,832,833,834,835,836,837,838,839,840,844,845,846,850,851,854,855,856,857,858,859,860,861,862,863,864,865,866,867,871,876,884,885,886,887,891,892,893,894,896,897,898,908,909,910,911,913,914,916,917,919,922,923,924,926,927,930,931,932,935,936,937,938,940,943,944,945,947,952,953,955,956,959,960,962,965,967,968,971,974,976,978,980,982,983,988,989,990,991,992,993,994,995,999,1000,1001,1002,1003,1004,1006,1007,1009,'..b'ATCCCCTGTCTGATTAA\tthrA\t[1618]\n+TTAATCAGACAGGGGATCTGGAACTGAGCAATGGG\tthrA\t[1618]\n+CCATTGCTCAGTTCCAGATCCCCTGTCTGATTAAA\tthrA\t[1618]\n+TTTAATCAGACAGGGGATCTGGAACTGAGCAATGG\tthrA\t[1618]\n+CATTGCTCAGTTCCAGATCCCCTGTCTGATTAAAA\tthrA\t[1618]\n+TTTTAATCAGACAGGGGATCTGGAACTGAGCAATG\tthrA\t[1618]\n+ATTGCTCAGTTCCAGATCCCCTGTCTGATTAAAAA\tthrA\t[1618]\n+TTTTTAATCAGACAGGGGATCTGGAACTGAGCAAT\tthrA\t[1618]\n+TTGCTCAGTTCCAGATCCCCTGTCTGATTAAAAAT\tthrA\t[1618]\n+ATTTTTAATCAGACAGGGGATCTGGAACTGAGCAA\tthrA\t[1618]\n+TGCTCAGTTCCAGATCCCCTGTCTGATTAAAAATA\tthrA\t[1618]\n+TATTTTTAATCAGACAGGGGATCTGGAACTGAGCA\tthrA\t[1618]\n+GCCGGACGCCAGGCTGTTGAAATCGATGTCCTACT\tthrA\t[1623]\n+AGTAGGACATCGATTTCAACAGCCTGGCGTCCGGC\tthrA\t[1623]\n+CCGGACGCCAGGCTGTTGAAATCGATGTCCTACTA\tthrA\t[1623]\n+TAGTAGGACATCGATTTCAACAGCCTGGCGTCCGG\tthrA\t[1623]\n+CGGACGCCAGGCTGTTGAAATCGATGTCCTACTAG\tthrA\t[1623]\n+CTAGTAGGACATCGATTTCAACAGCCTGGCGTCCG\tthrA\t[1623]\n+GGACGCCAGGCTGTTGAAATCGATGTCCTACTAGG\tthrA\t[1623]\n+CCTAGTAGGACATCGATTTCAACAGCCTGGCGTCC\tthrA\t[1623]\n+GACGCCAGGCTGTTGAAATCGATGTCCTACTAGGA\tthrA\t[1623]\n+TCCTAGTAGGACATCGATTTCAACAGCCTGGCGTC\tthrA\t[1623]\n+ACGCCAGGCTGTTGAAATCGATGTCCTACTAGGAA\tthrA\t[1623]\n+TTCCTAGTAGGACATCGATTTCAACAGCCTGGCGT\tthrA\t[1623]\n+CGCCAGGCTGTTGAAATCGATGTCCTACTAGGAAG\tthrA\t[1623]\n+CTTCCTAGTAGGACATCGATTTCAACAGCCTGGCG\tthrA\t[1623]\n+GCCAGGCTGTTGAAATCGATGTCCTACTAGGAAGC\tthrA\t[1623]\n+GCTTCCTAGTAGGACATCGATTTCAACAGCCTGGC\tthrA\t[1623]\n+CCAGGCTGTTGAAATCGATGTCCTACTAGGAAGCG\tthrA\t[1623]\n+CGCTTCCTAGTAGGACATCGATTTCAACAGCCTGG\tthrA\t[1623]\n+CAGGCTGTTGAAATCGATGTCCTACTAGGAAGCGA\tthrA\t[1623]\n+TCGCTTCCTAGTAGGACATCGATTTCAACAGCCTG\tthrA\t[1623]\n+AGGCTGTTGAAATCGATGTCCTACTAGGAAGCGAT\tthrA\t[1623]\n+ATCGCTTCCTAGTAGGACATCGATTTCAACAGCCT\tthrA\t[1623]\n+GGCTGTTGAAATCGATGTCCTACTAGGAAGCGATG\tthrA\t[1623]\n+CATCGCTTCCTAGTAGGACATCGATTTCAACAGCC\tthrA\t[1623]\n+GCTGTTGAAATCGATGTCCTACTAGGAAGCGATGG\tthrA\t[1623]\n+CCATCGCTTCCTAGTAGGACATCGATTTCAACAGC\tthrA\t[1623]\n+CTGTTGAAATCGATGTCCTACTAGGAAGCGATGGA\tthrA\t[1623]\n+TCCATCGCTTCCTAGTAGGACATCGATTTCAACAG\tthrA\t[1623]\n+TGTTGAAATCGATGTCCTACTAGGAAGCGATGGAG\tthrA\t[1623]\n+CTCCATCGCTTCCTAGTAGGACATCGATTTCAACA\tthrA\t[1623]\n+GTTGAAATCGATGTCCTACTAGGAAGCGATGGAGC\tthrA\t[1623]\n+GCTCCATCGCTTCCTAGTAGGACATCGATTTCAAC\tthrA\t[1623]\n+TTGAAATCGATGTCCTACTAGGAAGCGATGGAGCT\tthrA\t[1623]\n+AGCTCCATCGCTTCCTAGTAGGACATCGATTTCAA\tthrA\t[1623]\n+TGAAATCGATGTCCTACTAGGAAGCGATGGAGCTC\tthrA\t[1623]\n+GAGCTCCATCGCTTCCTAGTAGGACATCGATTTCA\tthrA\t[1623]\n+GAAATCGATGTCCTACTAGGAAGCGATGGAGCTCT\tthrA\t[1623]\n+AGAGCTCCATCGCTTCCTAGTAGGACATCGATTTC\tthrA\t[1623]\n+AAATCGATGTCCTACTAGGAAGCGATGGAGCTCTC\tthrA\t[1623]\n+GAGAGCTCCATCGCTTCCTAGTAGGACATCGATTT\tthrA\t[1623]\n+AATCGATGTCCTACTAGGAAGCGATGGAGCTCTCT\tthrA\t[1623]\n+AGAGAGCTCCATCGCTTCCTAGTAGGACATCGATT\tthrA\t[1623]\n+ATCGATGTCCTACTAGGAAGCGATGGAGCTCTCTT\tthrA\t[1623]\n+AAGAGAGCTCCATCGCTTCCTAGTAGGACATCGAT\tthrA\t[1623]\n+TCGATGTCCTACTAGGAAGCGATGGAGCTCTCTTA\tthrA\t[1623]\n+TAAGAGAGCTCCATCGCTTCCTAGTAGGACATCGA\tthrA\t[1623]\n+CGATGTCCTACTAGGAAGCGATGGAGCTCTCTTAC\tthrA\t[1623]\n+GTAAGAGAGCTCCATCGCTTCCTAGTAGGACATCG\tthrA\t[1623]\n+GATGTCCTACTAGGAAGCGATGGAGCTCTCTTACT\tthrA\t[1623]\n+AGTAAGAGAGCTCCATCGCTTCCTAGTAGGACATC\tthrA\t[1623]\n+ATGTCCTACTAGGAAGCGATGGAGCTCTCTTACTT\tthrA\t[1623]\n+AAGTAAGAGAGCTCCATCGCTTCCTAGTAGGACAT\tthrA\t[1623]\n+TGTCCTACTAGGAAGCGATGGAGCTCTCTTACTTC\tthrA\t[1623]\n+GAAGTAAGAGAGCTCCATCGCTTCCTAGTAGGACA\tthrA\t[1623]\n+GTCCTACTAGGAAGCGATGGAGCTCTCTTACTTCG\tthrA\t[1623]\n+CGAAGTAAGAGAGCTCCATCGCTTCCTAGTAGGAC\tthrA\t[1623]\n+TCCTACTAGGAAGCGATGGAGCTCTCTTACTTCGG\tthrA\t[1623]\n+CCGAAGTAAGAGAGCTCCATCGCTTCCTAGTAGGA\tthrA\t[1623]\n+CCTACTAGGAAGCGATGGAGCTCTCTTACTTCGGC\tthrA\t[1623]\n+GCCGAAGTAAGAGAGCTCCATCGCTTCCTAGTAGG\tthrA\t[1623]\n+CTACTAGGAAGCGATGGAGCTCTCTTACTTCGGCG\tthrA\t[1623]\n+CGCCGAAGTAAGAGAGCTCCATCGCTTCCTAGTAG\tthrA\t[1623]\n+TACTAGGAAGCGATGGAGCTCTCTTACTTCGGCGC\tthrA\t[1623]\n+GCGCCGAAGTAAGAGAGCTCCATCGCTTCCTAGTA\tthrA\t[1623]\n+ACTAGGAAGCGATGGAGCTCTCTTACTTCGGCGCT\tthrA\t[1623]\n+AGCGCCGAAGTAAGAGAGCTCCATCGCTTCCTAGT\tthrA\t[1623]\n+CTAGGAAGCGATGGAGCTCTCTTACTTCGGCGCTA\tthrA\t[1623]\n+TAGCGCCGAAGTAAGAGAGCTCCATCGCTTCCTAG\tthrA\t[1623]\n+TAGGAAGCGATGGAGCTCTCTTACTTCGGCGCTAA\tthrA\t[1623]\n+TTAGCGCCGAAGTAAGAGAGCTCCATCGCTTCCTA\tthrA\t[1623]\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_aroC.tfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_aroC.tfa Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,2512 @@\n+>aroC_1\n+GTTTTTCGCCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGCGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACTTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_2\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_3\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGTGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATTGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_4\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_5\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGCGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTTTTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_6\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGTATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_7\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_8\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAATTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGA'..b'GCAGGGGCGATCGCTAAGAAATACCTGGCGGAAAAGTTCGGTATCGAAATCCGCGGTTGTCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCAACAGGTTGAGCGTAATCCGTTCTTTTGCCCCGATGCGGATAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGCGACTCTATCGGCGCGAAAGTGACGGTGATAGCGAGCGGCGTGCCGGCAGGTCTTGGCGAACCGGTATTTGATCGGCTGGATGCGGATATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAAGGTGGTGGCGCTACGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_1565\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGAAAAAGTTCGGTATCGAAATCCGTGGCTGCCTGACCAAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAACTTAATCCGTTCTTTTGCCCCGATGCGGACAAACTTGATGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCAAGCGGCGTGCCGGCAGGTCTTGGCGAACCAGTATTTGACCGACTGGACGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGTGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGTCAGAATCGCGATGAAATCACGGCACAGGGT\n+>aroC_1567\n+GTCTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCACGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTAGCGGAAAAGTTCGGTATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGCGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTGTTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_1568\n+GTTTTTCGTCCGGGACACGCGGATTATACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATTGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGTGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_1569\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGTGGCGTGCCGGCAGGGCTTGGCGAACCGGTTTTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_1571\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATTGCCAAGAAATACCTAGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGCGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTTTTTGACCGACTGGATGCGGACATCGCCCATGGGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n+>aroC_1572\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGTGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATTGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGGAATCACGGCGCAGGGT\n+>aroC_1573\n+GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGTATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_config.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_config.txt Fri May 15 17:50:45 2026 +0000 |
| [ |
| @@ -0,0 +1,10 @@ +[loci] +aroC kmer/salmonella_aroC.tfa +dnaN kmer/salmonella_dnaN.tfa +hemD kmer/salmonella_hemD.tfa +hisD kmer/salmonella_hisD.tfa +purE kmer/salmonella_purE.tfa +sucA kmer/salmonella_sucA.tfa +thrA kmer/salmonella_thrA.tfa +[profile] +profile kmer/salmonella_profile.txt |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_dnaN.tfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_dnaN.tfa Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,2440 @@\n+>dnaN_1\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTTGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAGGCGTCTTTACCTAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGTGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_2\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGTGAAAACCCGCTGCGCGTGCAG\n+>dnaN_3\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGTTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_4\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_5\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCCACGCTTCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_6\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGTACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_7\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAATCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_8\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGTGCTACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACACTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGCAGCGAACTGCGCACTGTTGCGACCGACGGCCACCGTCTGGCGGT'..b'GAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_1326\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCTACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGCAGCGAACTGCGCACTGTTGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCATTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGTGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_1328\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAACGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGTGAAAACCCGCTGCGCGTGCAG\n+>dnaN_1329\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACACTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAAGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_1330\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCTACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCTTAATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGTTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_1331\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGTGCTACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGACGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_1333\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGTGCTACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGTCGTTCAGTTGGAAGGCGATCGGATGTTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n+>dnaN_1334\n+ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGTTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCACAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_hemD.tfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_hemD.tfa Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,2326 @@\n+>hemD_1\n+GCAACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACTCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGACGAAACTGGCCTGCGTCGCCGCGCTATTTCTCGATTGGCCGCACTACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGTTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_2\n+GCAACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACTCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGACGAAACTGGCCTGCGTCGCCGCGCTATTTCTCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGTTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_3\n+GCGACACTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_4\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGCCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_5\n+GCGACACTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTAATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_6\n+GCGACGCTCGCGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCGCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAAATGTTGCAA\n+>hemD_7\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTAATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_8\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_9\n+GCGACGCTGACGAAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGACACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATG'..b'GACGTTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCCCACGCCCAACTCCAGCGAGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGTCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGTCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGTCGCGAACTGCTGGGCGAAACCCTGACAGCTCACGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGAAGTGCGAAACATTACGATGGCGCAGAAGAGGCGATGCGCTGGCATACTCGCGGCGTAACGACGCTTGTTGTCACCAGCGGCGAGATGTTGCAA\n+>hemD_1265\n+GCGACTCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCTCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACACTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_1268\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGTGGCGCCGCGCTATTTTGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCGCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_1269\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGTGGCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCGCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGTGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_1270\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCCCACGCCCAGATCCAGCAGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGATTCGATATTCGTTATCCATTGGGTCGGGAAATCAGCGAAGTCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGTCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAATTTTTGTGAATGTTATCAACGAAGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATGCTCGCGGCATAACAACGCTTGTTGTCACCAGCGGCGAGATGTTGCAA\n+>hemD_1271\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGTGGCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCGCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_1272\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGTGGCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACACTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_1273\n+GCGAAGCTGACGGAAAAAGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCAAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n+>hemD_1275\n+GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACACCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTCACCAGCGGCGAGATGTTGCAA\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_hisD.tfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_hisD.tfa Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,3420 @@\n+>hisD_1\n+ATTGCGGGATGCCAGAAGGTGGTTCTGTGCTCGCCGCCACCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGGTGATCCTGCTGACGCCGGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGGCACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_2\n+ATTGCAGGATGCCAGATCGTGGTTCTGTGCTCGCCACCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCGTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_3\n+ATTGCGGGATGCCAGAAGGTGGTTCTGTGCTCGCCGCCACCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAATACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGGTGATCCTGCTGACGCCGGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGGCACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_4\n+ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGCCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCCCAGGTGATTCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAGCTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTAATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_5\n+ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCAGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGGTGATCCTACTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_6\n+ATTGCGGGATGCCAGAAGGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCAGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGATGATCCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_7\n+ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAACGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATTCTGCTGACGCCTGATGCTGACATTGCCTGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCAGAACTGCCGCGCGCGGACACCGCCAGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_8\n+ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCGGATGCTGACATTGCCCG'..b'GCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAATCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTCGTGACCGAAGCCAAACGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACGCCGGATTTCGTCGCTTCTGACCTGCTTTCCCAGGCAGAACACGGCCCGGATTCACAGGTGATTCTTCTGACGCCGGATGCCGACATCGCCCGCAAGGTAGCGGAGGCGGTAGAACGTCAACTGGCTGAACTGCCGCGCGCGGAAACCGCCCGTCAGGCTTTGCGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_1898\n+ATTGCGGGATGCCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCACAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCGTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTTGCAGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_1899\n+ATTGCGGGATGTCAGAAAGTGGTTCTGTGCTCGCCGCCGCCCATCGCCGATGAAATCCTCTATGCGGCACAACTGTGTGGCATACAGGAGATCTTTAACGTCGGCGGCTCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAATCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAATGCTTTTGTAACTGAAGCCAAGCGTCAGGTCAGTCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACGCCGGACTTCGTCGCTTCTGACCTGCTCTCCCAGGCAGAACACGGCCCGGATTCCCAGGTGATCCTGCTGACGCCGGATGCTAACATCGCCCGCAGGGTGGCGGAGGCGGTAGAACGTCAACTGGCTGAACTGCCGCGCGCGGACACCGCCCGTCAGGCTTTGCGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_1900\n+ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAACGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATTCTGCTGACGCCTGATGCTGACATTGCCTGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCAGAACTGCCGCGTGCGGACACCGCCAGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_1902\n+ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCGTCTGACCTGCTCTCCCAGGCAGAACACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCTGATGCTCACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_1903\n+ATTGCGGGATGCCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCACGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCCCAGGTGATTCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_1904\n+ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCGGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCGTCTGACCTGCTCTCCCAAGCTGAGCACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCGGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAGCTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n+>hisD_1905\n+ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCACAGCTATGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCACAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAATCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAATGCTTTTGTAACTGAAGCCAAGCGTCAGGTCAGTCAGCGTCTCGACGGCGTGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACGCCGGACTTCGTCGCTTCTGACCTGCTCTCCCAGGCAGAACACGGCCCGGATTCCCAGGTGATCCTGCTGACGCCGGATGCTGACATCGCCCGCAGGGTGGCGGAGGCGGTAGAACGTCAACTGGCTGAACTGCCGCGCGCGGACACCGCCCGTCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_profile.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_profile.txt Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,9123 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|
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_purE.tfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_purE.tfa Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,2708 @@\n+>purE_1\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCACACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGGGCGGCGAACGCCGCACTGCTGGCAGCGCAAATTTTGGCTACGCATGATAGCGCGCTGCATCGGCGCATCGCCGAC\n+>purE_2\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n+>purE_3\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACACTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCACAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCCGAC\n+>purE_4\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n+>purE_5\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_6\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_7\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTTTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_8\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_9\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTTTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACACTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n+>purE_10\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCACATCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTACCGGTACAAAGCGCTGCGCTAAGCGGTGTGGATAGCCTCTACTCCATCGTGCAGATG'..b'TCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_1560\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_1562\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGGGCGGCGAACGCCGCACTGCTGGCAGCGCAAATTTTGGCTACGCATGATAGCGCGCTGCATCGGCGCATCGCCGAC\n+>purE_1563\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCAGTGGGTACGCTGGCGATCGGCAAAGCCGGTGCCGCGAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCCGAC\n+>purE_1564\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_1565\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_1566\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_1568\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTCTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTTTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n+>purE_1569\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCACACCTGCCGGGAATGATTGCGGCAAAAACTCTGGTCCCGGTACTCGGCGTACCGGTACAAAGCGCTGCGCTAAGCGGTGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCACTGCTGGCAGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n+>purE_1570\n+AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGGGCGGGCGGCGCGGCACACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_sucA.tfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_sucA.tfa Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,2532 @@\n+>sucA_1\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCTATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGTCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTTGCCGGTAAACATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACTGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACCGACTGGACGAACCGAGCAGTAATAAAGTGCTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_2\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGCTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_3\n+AAACGTTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATTACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_4\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACTGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCACCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGTGCCCGTCTGGACCGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATTACCATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_5\n+AAACGTTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGAACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTTGCCGGTAAACATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCACCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGTGCCCGTCTGGACCGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_6\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_7\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_8\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCCGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGTGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACTGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGT'..b'CCGATGCTGAAAGAGATGGTTCGCCATGCGGGTAATAGCGGCACTCGCGAAGTGGTGCTGGGTATGGCGCACCGCGGTCGCCTGAACGTACTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTTGCCGGTAAGCATAAAGAACATCTTGGCACCGGCGATGTGAAGTACCACATGGGCTTCTCGTCAGATATCGAAACGGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCACCTGGAAATCGTGAGCCCGGTGGTGATGGGATCTGTGCGTGCGCGTTTGGATAGACTGGACGAACCGAGCAGCAACAAAGTGCTACCCATCACCATTCATGGCGATGCGGCAGTCACCGGCCAGGGCGTGGTTCAG\n+>sucA_1409\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCAGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_1410\n+AAACGCTTTCTGAACGAACTAACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCCGGTGCGAAACGTTTCTCGCTGGAGGGGGGAGATGCTCTGGTACCCATGTTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGGTCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTTGCCGGTAAGCATAAAGAACATCTTGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGCCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCACCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGTGCTCGTCTGGACAGACTGGACGAGCCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_1411\n+AAACGTTTCCTAAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATTTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_1412\n+AAACGTTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCACTGGCGTTTAACCCATCGCATTTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_1415\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATTTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGTGCCCGTCTGGACCGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_1416\n+AAACGTTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGTTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATTTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n+>sucA_1417\n+AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGTGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACTGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACCGACTGGACGAACCGAGCAGTAATAAAGTGCTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n' |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_thrA.tfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_thrA.tfa Fri May 15 17:50:45 2026 +0000 |
| b |
| b'@@ -0,0 +1,2946 @@\n+>thrA_1\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGACTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_2\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAACCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_3\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCATCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_4\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCACGTCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCATCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_5\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACCAGGAAGCGATGGAGCTCTCTTACTTCGGCGCTAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_6\n+GTGCTGGGGCGTAATGGCTCTGACTACTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGACTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTGAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCTGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_7\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTTCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTCAAAGGGATCTCTAACCTTAACAATATGGCGATGTTTAGCGTCTCCGGCCCTGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_8\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACCAGGAAGCGATGGAGCTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGAT'..b'CCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_1615\n+GTGCTTGGGCGTAATGGCTCTGACTACTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACCAGGAAGCGATGGAGCTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCAGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCAGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_1616\n+GTACTGGGCCGTAACGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCGTGTTTACGTGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATGATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGTCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTACTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_1617\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTTCTTCACCCTCGTACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAACCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_1618\n+GTGCTGGGCCGTAATGGTTCCGACTATTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATTGCTCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTACTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_1621\n+GTGCTGGGGCGTAATGGCTCTGACTACTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGTGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGTGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCTGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_1623\n+GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACTAGGAAGCGATGGAGCTCTCTTACTTCGGCGCTAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n+>thrA_1624\n+GTGCTGGGGCGTAATGGCTCTGACTACTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGTGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGAATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n' |
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| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/kmer/salmonella_weight.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/seqsero2s_db/kmer/salmonella_weight.txt Fri May 15 17:50:45 2026 +0000 |
| b |
| @@ -0,0 +1,9 @@ +purE_631 0.7904408017272534 +purE_748 0.83309951166174 +purE_749 0.7904408017272534 +purE_781 0.8757582215962267 +purE_866 0.7904408017272534 +purE_868 0.8180434963907447 +purE_971 1.076505091876164 +purE_1502 0.83309951166174 +purE_1537 1.0539210689696712 |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/mlst.pickle |
| b |
| Binary file SeqSero2S/seqsero2s_db/mlst.pickle has changed |
| b |
| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/seqsero2s_db/special.pickle |
| b |
| Binary file SeqSero2S/seqsero2s_db/special.pickle has changed |
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| diff -r 6ae6c7a51b22 -r cfc91e1d2c9b SeqSero2S/setup.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2S/setup.py Fri May 15 17:50:45 2026 +0000 |
| [ |
| @@ -0,0 +1,31 @@ +import os, sys +from distutils.core import setup +from setuptools import find_packages + +def readme(): + with open('README.md') as f: + return f.read() + +setup(name='SeqSero2S', + #version=open("version.py").readlines()[-1].split()[-1].strip("\"'"), + version='1.1.4', + description='Salmonella serotyping', + long_description=readme(), + classifiers=[ + 'Development Status :: 3 - Alpha', + 'License :: OSI Approved :: GNU General Public License v2 (GPLv2)', + 'Programming Language :: Python :: 3', + 'Topic :: Text Processing :: Linguistic', + ], + keywords='Salmonella serotyping bioinformatics WGS', + url='https://github.com/denglab/SeqSero2S/', + author='Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng', + author_email='zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu', + license='GPLv2', + scripts=["bin/deinterleave_fastq.sh","bin/Initial_Conditions_SS2S.py","bin/Initial_Conditions_SS2.py","bin/SeqSero2S.py","bin/SeqSero2_update_kmer_database.py"], + packages=[""], + include_package_data = True, + install_requires=['biopython~=1.73'], + data_files=[("seqsero2s_db",["seqsero2s_db/mlst.pickle","seqsero2s_db/antigens.pickle","seqsero2s_db/H_and_O_and_specific_genes.fasta","seqsero2s_db/invA_mers_dict","seqsero2s_db/special.pickle"]),("seqsero2s_db/kmer",["seqsero2s_db/kmer/salmonella_35.txt","seqsero2s_db/kmer/salmonella_config.txt","seqsero2s_db/kmer/salmonella_hemD.tfa","seqsero2s_db/kmer/salmonella.log","seqsero2s_db/kmer/salmonella_purE.tfa","seqsero2s_db/kmer/salmonella_thrA.tfa","seqsero2s_db/kmer/salmonella_aroC.tfa","seqsero2s_db/kmer/salmonella_dnaN.tfa","seqsero2s_db/kmer/salmonella_hisD.tfa","seqsero2s_db/kmer/salmonella_profile.txt","seqsero2s_db/kmer/salmonella_sucA.tfa","seqsero2s_db/kmer/salmonella_weight.txt"])], + zip_safe=False, +) |